Fig. 5: Long-term epigenetic and transcriptional consequences of exposure of a chromosome to the cytoplasm.

a, Generation of RPE-1 clones with broken chromosome 4 and control RPE-1 clones. Chromosome 4 bridges were generated by sister chromatid fusion after CRISPR–Cas9 breakage at the subtelomeres of either 4p or 4q (left, bottom to top). ATAC-seq, RNA-seq and DNA-seq were performed on the bridge clones, control clones, and bulk (parental population) controls. b, Average ATAC signal variation in 10 Mb intervals in control (n = 10) and bridge clones (n = 12). White dots indicate the median; black boxes indicate first and third quantiles; red dots indicate a 10 Mb region on chromosome 4 (27–37 Mb) with significantly reduced chromatin accessibility in bridge clones. Regions with significantly reduced ATAC intensities in the control clones (fold change < 0.65) are from pericentric regions of chromosome 1, chromosome 9 and chromosome 15 with few ATAC peaks. c, Copy number normalized ATAC-seq peak intensities in chromosome 4 (26–38 Mb) in the parental clone, control clones and bridge clones. The region with an asterisk in bridge clone III has DNA copy number zero from homozygous deletion and is masked. See Extended Data Fig. 11 for haplotype-specific DNA copy number alterations and rearrangements in bridge clones. There is a significant reduction in the ATAC signal in 6 out of 12 clones (I–V and XII) (P < 0.0001, one-sided permutation test; Methods). Bridge clones are ordered by the level of PCDH7 expression (ascending), the only gene with significant expression within this region. Arrow indicates the PCDH7 promoter. d, Correlation between PCDH7 expression (log-transformed transcripts per million ratio) and chromatin accessibility in the promoter and gene body of PCDH7 (normalized ATAC peak intensity) in control (green dots) and bridge clones (purple dots). Four bridge clones displaying a reduction in both chromatin accessibility and gene expression are on the lower left labelled with sample identifiers.